- How many reads are properly paired?
samtools view -F 0x0002 untreated3.bam -bo - | samtools sort -n - untreated3_paired
samtools view untreated3_paired.bam | wc -l
# 13,212,182 / 2 = 6,606,091- How would you sort the properly paired reads by name instead?
samtools sort -n untreated3_paired.bam | head- Which percentage of those properly paired reads map uniquely?
samtools view -q 255 untreated3_paired.bam | wc -l
# 7,417,488 / 2= 3,708,744